9NTG | pdb_00009ntg

Helix pomatia AMP deaminase (HPAMPD) in complex with Pentostatin

PDB DOI: https://doi.org/10.2210/pdb9NTG/pdb

Classification: HYDROLASE
Organism(s): Helix pomatia
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2025-03-18 Released: 2025-06-18
Deposition Author(s): Kaur, G., Horton, J.R., Cheng, X.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Cancer Prevention and Research Institute of Texas (CPRIT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free:
0.182 (Depositor), 0.182 (DCC)
R-Value Work:
0.156 (Depositor), 0.156 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Helix pomatia AMP deaminase (HPAMPD) in complex with Pentostatin (DCF)

Kaur, G., Horton, J.R., Cheng, X.

To be published.

Macromolecule Content

Total Structure Weight: 253.67 kDa
Atom Count: 18,921
Modeled Residue Count: 1,996
Deposited Residue Count: 2,164
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Helix pomatia AMP deaminase	A, B, C, D	541	Helix pomatia	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DCF (Subject of Investigation/LOI) Query on DCF Download Ideal Coordinates CCD File SDF format, chain CC [auth D] SDF format, chain LB [auth C] SDF format, chain UA [auth B] SDF format, chain V [auth A] MOL2 format, chain CC [auth D] MOL2 format, chain LB [auth C] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] mmCIF format, chain CC [auth D] mmCIF format, chain LB [auth C] mmCIF format, chain UA [auth B] mmCIF format, chain V [auth A]	CC [auth D], LB [auth C], UA [auth B], V [auth A]	2'-DEOXYCOFORMYCIN C₁₁ H₁₆ N₄ O₄ FPVKHBSQESCIEP-JQCXWYLXSA-N		Interactions Focus chain CC [auth D] Focus chain LB [auth C] Focus chain UA [auth B] Focus chain V [auth A] Interactions & Density Focus chain CC [auth D] Focus chain LB [auth C] Focus chain UA [auth B] Focus chain V [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain MB [auth D] SDF format, chain NB [auth D] SDF format, chain OB [auth D] SDF format, chain PB [auth D] SDF format, chain VA [auth C] SDF format, chain W [auth B] SDF format, chain WA [auth C] SDF format, chain X [auth B] SDF format, chain XA [auth C] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain MB [auth D] MOL2 format, chain NB [auth D] MOL2 format, chain OB [auth D] MOL2 format, chain PB [auth D] MOL2 format, chain VA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain MB [auth D] mmCIF format, chain NB [auth D] mmCIF format, chain OB [auth D] mmCIF format, chain PB [auth D] mmCIF format, chain VA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] MB [auth D] F [auth A], G [auth A], H [auth A], I [auth A], MB [auth D], NB [auth D], OB [auth D], PB [auth D], VA [auth C], W [auth B], WA [auth C], X [auth B], XA [auth C], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain MB [auth D] Focus chain NB [auth D] Focus chain OB [auth D] Focus chain PB [auth D] Focus chain VA [auth C] Focus chain W [auth B] Focus chain WA [auth C] Focus chain X [auth B] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain MB [auth D] Focus chain NB [auth D] Focus chain OB [auth D] Focus chain PB [auth D] Focus chain VA [auth C] Focus chain W [auth B] Focus chain WA [auth C] Focus chain X [auth B] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain Z [auth B]
BTB Query on BTB Download Ideal Coordinates CCD File SDF format, chain JA [auth B] SDF format, chain N [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain N [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain N [auth A]	JA [auth B], N [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain JA [auth B] Focus chain N [auth A] Interactions & Density Focus chain JA [auth B] Focus chain N [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain J [auth A] SDF format, chain QB [auth D] SDF format, chain YA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain QB [auth D] MOL2 format, chain YA [auth C] mmCIF format, chain AA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain QB [auth D] mmCIF format, chain YA [auth C]	AA [auth B], J [auth A], QB [auth D], YA [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain J [auth A] Focus chain QB [auth D] Focus chain YA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain J [auth A] Focus chain QB [auth D] Focus chain YA [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain AC [auth D] SDF format, chain BA [auth B] SDF format, chain BB [auth C] SDF format, chain BC [auth D] SDF format, chain CA [auth B] SDF format, chain CB [auth C] SDF format, chain DA [auth B] SDF format, chain DB [auth C] SDF format, chain EA [auth B] SDF format, chain EB [auth C] SDF format, chain FA [auth B] SDF format, chain FB [auth C] SDF format, chain GA [auth B] SDF format, chain GB [auth C] SDF format, chain HA [auth B] SDF format, chain HB [auth C] SDF format, chain IA [auth B] SDF format, chain IB [auth C] SDF format, chain JB [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain KB [auth C] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain RB [auth D] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain SB [auth D] SDF format, chain T [auth A] SDF format, chain TB [auth D] SDF format, chain U [auth A] SDF format, chain UB [auth D] SDF format, chain VB [auth D] SDF format, chain WB [auth D] SDF format, chain XB [auth D] SDF format, chain YB [auth D] SDF format, chain ZA [auth C] SDF format, chain ZB [auth D] SDF format, chain L [auth A] SDF format, chain TA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain AC [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain BC [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth C] MOL2 format, chain JB [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth C] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain RB [auth D] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain SB [auth D] MOL2 format, chain T [auth A] MOL2 format, chain TB [auth D] MOL2 format, chain U [auth A] MOL2 format, chain UB [auth D] MOL2 format, chain VB [auth D] MOL2 format, chain WB [auth D] MOL2 format, chain XB [auth D] MOL2 format, chain YB [auth D] MOL2 format, chain ZA [auth C] MOL2 format, chain ZB [auth D] MOL2 format, chain L [auth A] MOL2 format, chain TA [auth B] mmCIF format, chain AB [auth C] mmCIF format, chain AC [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain BC [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth C] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth C] mmCIF format, chain FA [auth B] mmCIF format, chain FB [auth C] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain HB [auth C] mmCIF format, chain IA [auth B] mmCIF format, chain IB [auth C] mmCIF format, chain JB [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain KB [auth C] mmCIF format, chain LA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain RB [auth D] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain SB [auth D] mmCIF format, chain T [auth A] mmCIF format, chain TB [auth D] mmCIF format, chain U [auth A] mmCIF format, chain UB [auth D] mmCIF format, chain VB [auth D] mmCIF format, chain WB [auth D] mmCIF format, chain XB [auth D] mmCIF format, chain YB [auth D] mmCIF format, chain ZA [auth C] mmCIF format, chain ZB [auth D] mmCIF format, chain L [auth A] mmCIF format, chain TA [auth B]	AB [auth C] AC [auth D] BA [auth B] BB [auth C] BC [auth D] AB [auth C], AC [auth D], BA [auth B], BB [auth C], BC [auth D], CA [auth B], CB [auth C], DA [auth B], DB [auth C], EA [auth B], EB [auth C], FA [auth B], FB [auth C], GA [auth B], GB [auth C], HA [auth B], HB [auth C], IA [auth B], IB [auth C], JB [auth C], K [auth A], KA [auth B], KB [auth C], L [auth A], LA [auth B], M [auth A], MA [auth B], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], RB [auth D], S [auth A], SA [auth B], SB [auth D], T [auth A], TA [auth B], TB [auth D], U [auth A], UB [auth D], VB [auth D], WB [auth D], XB [auth D], YB [auth D], ZA [auth C], ZB [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth C] Focus chain AC [auth D] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain BC [auth D] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth D] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth D] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth D] Focus chain U [auth A] Focus chain UB [auth D] Focus chain VB [auth D] Focus chain WB [auth D] Focus chain XB [auth D] Focus chain YB [auth D] Focus chain ZA [auth C] Focus chain ZB [auth D] Interactions & Density Focus chain AB [auth C] Focus chain AC [auth D] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain BC [auth D] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth D] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth D] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth D] Focus chain U [auth A] Focus chain UB [auth D] Focus chain VB [auth D] Focus chain WB [auth D] Focus chain XB [auth D] Focus chain YB [auth D] Focus chain ZA [auth C] Focus chain ZB [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.182 (Depositor), 0.182 (DCC)
R-Value Work: 0.156 (Depositor), 0.156 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.128	α = 90
b = 81.983	β = 92.265
c = 212.016	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-18

Deposition Author(s):

Kaur, G.

Horton, J.R.

Cheng, X.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM134744
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RR160029